PGS1

phosphatidylglycerophosphate synthase 1

Basic information

Region (hg38): 17:78378648-78425114

Links

ENSG00000087157 ∙ NCBI:9489 ∙ OMIM:614942 ∙ HGNC:30029 ∙ Uniprot:Q32NB8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGS1 gene.

• Inborn genetic diseases (26 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGS1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	3	5	15
Total	0	0	26	4	5

Variants in PGS1

This is a list of pathogenic ClinVar variants found in the PGS1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-78378669-G-A		not specified	Uncertain significance (Mar 17, 2023)
17-78378679-C-A		not specified	Uncertain significance (Jan 30, 2024)
17-78378702-T-C		not specified	Uncertain significance (Mar 29, 2022)
17-78378774-C-T		not specified	Uncertain significance (Oct 05, 2023)
17-78378805-G-T		not specified	Uncertain significance (Dec 11, 2023)
17-78396345-C-T		not specified	Uncertain significance (Jun 06, 2023)
17-78398258-T-C		not specified	Uncertain significance (Jan 04, 2024)
17-78398337-C-A		not specified	Uncertain significance (Aug 19, 2023)
17-78399348-G-C		not specified	Uncertain significance (Jun 22, 2021)
17-78399387-G-A		not specified	Likely benign (Sep 06, 2022)
17-78399426-C-A		not specified	Uncertain significance (Apr 28, 2023)
17-78399429-C-T		not specified	Uncertain significance (May 31, 2023)
17-78399450-G-A		not specified	Uncertain significance (Jan 22, 2024)
17-78400718-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-78400763-C-T		not specified	Uncertain significance (Jun 03, 2022)
17-78400778-C-T		not specified	Uncertain significance (Jun 01, 2023)
17-78403573-C-T		not specified	Uncertain significance (Feb 06, 2024)
17-78403598-A-G		not specified	Uncertain significance (Oct 26, 2021)
17-78403691-A-G		not specified	Uncertain significance (Feb 05, 2024)
17-78403697-C-G		not specified	Uncertain significance (Jul 06, 2021)
17-78403724-C-A		not specified	Uncertain significance (Dec 08, 2023)
17-78403793-C-T		not specified	Uncertain significance (Aug 08, 2023)
17-78403873-A-G		not specified	Uncertain significance (Dec 21, 2022)
17-78403907-A-G		not specified	Uncertain significance (Apr 25, 2022)
17-78403966-G-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGS1	protein_coding	protein_coding	ENST00000262764	9	46475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-11	0.316	124868	0	50	124918	0.000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	254	331	0.768	0.0000211	3554
Missense in Polyphen		68	89.599	0.75894		864
Synonymous	-0.670	155	145	1.07	0.00000934	1178
Loss of Function	1.04	20	25.7	0.778	0.00000137	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000395	0.000389
Ashkenazi Jewish	0.000596	0.000596
East Asian	0.000111	0.000111
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000162	0.000159
Middle Eastern	0.000111	0.000111
South Asian	0.000262	0.000261
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin. {ECO:0000250}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Phospholipid Biosynthesis;Metabolism of lipids;cardiolipin biosynthesis;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PG (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.361
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.395
• hipred: Y
• hipred_score: 0.541
• ghis: 0.559

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.395

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pgs1
• Phenotype: vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: phosphatidylglycerol biosynthetic process;cardiolipin biosynthetic process;diacylglycerol metabolic process
• Cellular component: mitochondrion;mitochondrial inner membrane;endoplasmic reticulum
• Molecular function: calcium ion binding;ATP binding;CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity